Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 10:27:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh5_11214/10_2023/6zh5_11214.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 16 7.16 5 S 96 5.16 5 C 21480 2.51 5 N 6192 2.21 5 O 6624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z GLU 46": "OE1" <-> "OE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z ASP 72": "OD1" <-> "OD2" Residue "Z ASP 88": "OD1" <-> "OD2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 138": "OE1" <-> "OE2" Residue "Z GLU 172": "OE1" <-> "OE2" Residue "Z ASP 183": "OD1" <-> "OD2" Residue "Z GLU 187": "OE1" <-> "OE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 58": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J ASP 183": "OD1" <-> "OD2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K GLU 131": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K GLU 172": "OE1" <-> "OE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L ASP 183": "OD1" <-> "OD2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "M GLU 131": "OE1" <-> "OE2" Residue "M GLU 138": "OE1" <-> "OE2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M GLU 187": "OE1" <-> "OE2" Residue "N GLU 12": "OE1" <-> "OE2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O GLU 138": "OE1" <-> "OE2" Residue "O GLU 172": "OE1" <-> "OE2" Residue "O ASP 183": "OD1" <-> "OD2" Residue "O GLU 187": "OE1" <-> "OE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P ASP 88": "OD1" <-> "OD2" Residue "P GLU 131": "OE1" <-> "OE2" Residue "P GLU 138": "OE1" <-> "OE2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "P ASP 183": "OD1" <-> "OD2" Residue "P GLU 187": "OE1" <-> "OE2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q GLU 131": "OE1" <-> "OE2" Residue "Q GLU 138": "OE1" <-> "OE2" Residue "Q GLU 172": "OE1" <-> "OE2" Residue "Q ASP 183": "OD1" <-> "OD2" Residue "Q GLU 187": "OE1" <-> "OE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R ASP 88": "OD1" <-> "OD2" Residue "R GLU 131": "OE1" <-> "OE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 172": "OE1" <-> "OE2" Residue "R ASP 183": "OD1" <-> "OD2" Residue "R GLU 187": "OE1" <-> "OE2" Residue "S GLU 12": "OE1" <-> "OE2" Residue "S ARG 40": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 54": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S ASP 88": "OD1" <-> "OD2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "S GLU 172": "OE1" <-> "OE2" Residue "S ASP 183": "OD1" <-> "OD2" Residue "S GLU 187": "OE1" <-> "OE2" Residue "T GLU 12": "OE1" <-> "OE2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "T ASP 88": "OD1" <-> "OD2" Residue "T GLU 131": "OE1" <-> "OE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "T GLU 172": "OE1" <-> "OE2" Residue "T ASP 183": "OD1" <-> "OD2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U GLU 12": "OE1" <-> "OE2" Residue "U ARG 40": "NH1" <-> "NH2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U ASP 72": "OD1" <-> "OD2" Residue "U ASP 88": "OD1" <-> "OD2" Residue "U GLU 131": "OE1" <-> "OE2" Residue "U GLU 138": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U ASP 183": "OD1" <-> "OD2" Residue "U GLU 187": "OE1" <-> "OE2" Residue "V GLU 12": "OE1" <-> "OE2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 54": "OE1" <-> "OE2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V ASP 88": "OD1" <-> "OD2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V ASP 183": "OD1" <-> "OD2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "W GLU 12": "OE1" <-> "OE2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W GLU 58": "OE1" <-> "OE2" Residue "W ASP 72": "OD1" <-> "OD2" Residue "W ASP 88": "OD1" <-> "OD2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 138": "OE1" <-> "OE2" Residue "W GLU 172": "OE1" <-> "OE2" Residue "W ASP 183": "OD1" <-> "OD2" Residue "W GLU 187": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 138": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 34408 Number of models: 1 Model: "" Number of chains: 35 Chain: "Z" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "G" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "I" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "K" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "L" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "M" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "N" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "O" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "P" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "Q" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "S" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "T" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "U" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "V" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "W" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "F" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1433 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.77, per 1000 atoms: 0.49 Number of scatterers: 34408 At special positions: 0 Unit cell: (128.7, 128.7, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 16 26.01 S 96 16.00 O 6624 8.00 N 6192 7.00 C 21480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.86 Conformation dependent library (CDL) restraints added in 4.8 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'Z' and resid 10 through 36 Processing helix chain 'Z' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU Z 58 " --> pdb=" O GLU Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA Z 99 " --> pdb=" O GLU Z 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET Z 103 " --> pdb=" O ALA Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 123 through 134 Processing helix chain 'Z' and resid 134 through 155 Processing helix chain 'Z' and resid 170 through 179 Processing helix chain 'Z' and resid 179 through 191 removed outlier: 3.728A pdb=" N ILE Z 186 " --> pdb=" O HIS Z 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 36 Processing helix chain 'A' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 155 Processing helix chain 'C' and resid 170 through 179 Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 36 Processing helix chain 'E' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 155 Processing helix chain 'E' and resid 170 through 179 Processing helix chain 'E' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 155 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 36 Processing helix chain 'H' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 155 Processing helix chain 'H' and resid 170 through 179 Processing helix chain 'H' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE H 186 " --> pdb=" O HIS H 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU I 58 " --> pdb=" O GLU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA I 99 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET I 103 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 155 Processing helix chain 'I' and resid 170 through 179 Processing helix chain 'I' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE I 186 " --> pdb=" O HIS I 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 36 Processing helix chain 'J' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET J 103 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 155 Processing helix chain 'J' and resid 170 through 179 Processing helix chain 'J' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE J 186 " --> pdb=" O HIS J 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 36 Processing helix chain 'K' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA K 99 " --> pdb=" O GLU K 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET K 103 " --> pdb=" O ALA K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 155 Processing helix chain 'K' and resid 170 through 179 Processing helix chain 'K' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE K 186 " --> pdb=" O HIS K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 36 Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU L 58 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA L 99 " --> pdb=" O GLU L 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 155 Processing helix chain 'L' and resid 170 through 179 Processing helix chain 'L' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA M 99 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET M 103 " --> pdb=" O ALA M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 155 Processing helix chain 'M' and resid 170 through 179 Processing helix chain 'M' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE M 186 " --> pdb=" O HIS M 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 36 Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA N 99 " --> pdb=" O GLU N 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET N 103 " --> pdb=" O ALA N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 155 Processing helix chain 'N' and resid 170 through 179 Processing helix chain 'N' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE N 186 " --> pdb=" O HIS N 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 36 Processing helix chain 'O' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA O 99 " --> pdb=" O GLU O 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET O 103 " --> pdb=" O ALA O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 155 Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE O 186 " --> pdb=" O HIS O 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 36 Processing helix chain 'P' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU P 58 " --> pdb=" O GLU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA P 99 " --> pdb=" O GLU P 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET P 103 " --> pdb=" O ALA P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 155 Processing helix chain 'P' and resid 170 through 179 Processing helix chain 'P' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE P 186 " --> pdb=" O HIS P 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 36 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.697A pdb=" N GLU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA Q 99 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET Q 103 " --> pdb=" O ALA Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 155 Processing helix chain 'Q' and resid 170 through 179 Processing helix chain 'Q' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE Q 186 " --> pdb=" O HIS Q 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 36 Processing helix chain 'R' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU R 58 " --> pdb=" O GLU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA R 99 " --> pdb=" O GLU R 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 155 Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'R' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE R 186 " --> pdb=" O HIS R 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 36 Processing helix chain 'S' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU S 58 " --> pdb=" O GLU S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 121 removed outlier: 3.628A pdb=" N ALA S 99 " --> pdb=" O GLU S 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET S 103 " --> pdb=" O ALA S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 155 Processing helix chain 'S' and resid 170 through 179 Processing helix chain 'S' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE S 186 " --> pdb=" O HIS S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 36 Processing helix chain 'T' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU T 58 " --> pdb=" O GLU T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA T 99 " --> pdb=" O GLU T 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET T 103 " --> pdb=" O ALA T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 155 Processing helix chain 'T' and resid 170 through 179 Processing helix chain 'T' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE T 186 " --> pdb=" O HIS T 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 36 Processing helix chain 'U' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 121 removed outlier: 3.630A pdb=" N ALA U 99 " --> pdb=" O GLU U 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET U 103 " --> pdb=" O ALA U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 155 Processing helix chain 'U' and resid 170 through 179 Processing helix chain 'U' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE U 186 " --> pdb=" O HIS U 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 36 Processing helix chain 'V' and resid 45 through 73 removed outlier: 3.699A pdb=" N GLU V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA V 99 " --> pdb=" O GLU V 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET V 103 " --> pdb=" O ALA V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 155 Processing helix chain 'V' and resid 170 through 179 Processing helix chain 'V' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE V 186 " --> pdb=" O HIS V 182 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 36 Processing helix chain 'W' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA W 99 " --> pdb=" O GLU W 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET W 103 " --> pdb=" O ALA W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 155 Processing helix chain 'W' and resid 170 through 179 Processing helix chain 'W' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE W 186 " --> pdb=" O HIS W 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 36 Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 155 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.726A pdb=" N ILE B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 Processing helix chain 'D' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 155 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.728A pdb=" N ILE D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 36 Processing helix chain 'F' and resid 45 through 73 removed outlier: 3.698A pdb=" N GLU F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 121 removed outlier: 3.629A pdb=" N ALA F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 155 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 179 through 191 removed outlier: 3.727A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.68 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12024 1.34 - 1.46: 7168 1.46 - 1.57: 15584 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 34944 Sorted by residual: bond pdb=" CG ARG G 121 " pdb=" CD ARG G 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG V 121 " pdb=" CD ARG V 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG T 121 " pdb=" CD ARG T 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CG ARG U 121 " pdb=" CD ARG U 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CG ARG L 121 " pdb=" CD ARG L 121 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 34939 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 575 107.14 - 113.85: 19823 113.85 - 120.55: 15274 120.55 - 127.26: 11008 127.26 - 133.97: 264 Bond angle restraints: 46944 Sorted by residual: angle pdb=" CB ARG O 121 " pdb=" CG ARG O 121 " pdb=" CD ARG O 121 " ideal model delta sigma weight residual 111.30 121.53 -10.23 2.30e+00 1.89e-01 1.98e+01 angle pdb=" CB ARG C 121 " pdb=" CG ARG C 121 " pdb=" CD ARG C 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG H 121 " pdb=" CG ARG H 121 " pdb=" CD ARG H 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG L 121 " pdb=" CG ARG L 121 " pdb=" CD ARG L 121 " ideal model delta sigma weight residual 111.30 121.52 -10.22 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB ARG G 121 " pdb=" CG ARG G 121 " pdb=" CD ARG G 121 " ideal model delta sigma weight residual 111.30 121.50 -10.20 2.30e+00 1.89e-01 1.97e+01 ... (remaining 46939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 18000 16.82 - 33.63: 1920 33.63 - 50.45: 816 50.45 - 67.27: 264 67.27 - 84.08: 96 Dihedral angle restraints: 21096 sinusoidal: 8736 harmonic: 12360 Sorted by residual: dihedral pdb=" CB GLU J 61 " pdb=" CG GLU J 61 " pdb=" CD GLU J 61 " pdb=" OE1 GLU J 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.08 84.08 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU E 61 " pdb=" CG GLU E 61 " pdb=" CD GLU E 61 " pdb=" OE1 GLU E 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.07 84.07 1 3.00e+01 1.11e-03 9.57e+00 dihedral pdb=" CB GLU Z 61 " pdb=" CG GLU Z 61 " pdb=" CD GLU Z 61 " pdb=" OE1 GLU Z 61 " ideal model delta sinusoidal sigma weight residual 0.00 -84.05 84.05 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2144 0.025 - 0.050: 1797 0.050 - 0.076: 806 0.076 - 0.101: 239 0.101 - 0.126: 54 Chirality restraints: 5040 Sorted by residual: chirality pdb=" CB VAL C 139 " pdb=" CA VAL C 139 " pdb=" CG1 VAL C 139 " pdb=" CG2 VAL C 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CB VAL H 139 " pdb=" CA VAL H 139 " pdb=" CG1 VAL H 139 " pdb=" CG2 VAL H 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CB VAL I 139 " pdb=" CA VAL I 139 " pdb=" CG1 VAL I 139 " pdb=" CG2 VAL I 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 5037 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 121 " -0.041 9.50e-02 1.11e+02 2.37e-02 2.96e+00 pdb=" NE ARG B 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG B 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 121 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.90e+00 pdb=" NE ARG F 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 121 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.90e+00 pdb=" NE ARG H 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG H 121 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG H 121 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 357 2.59 - 3.17: 30265 3.17 - 3.75: 57123 3.75 - 4.32: 81669 4.32 - 4.90: 132530 Nonbonded interactions: 301944 Sorted by model distance: nonbonded pdb=" OE1 GLU I 131 " pdb="FE FE I 202 " model vdw 2.015 2.260 nonbonded pdb=" OE1 GLU H 131 " pdb="FE FE H 201 " model vdw 2.018 2.260 nonbonded pdb=" OE1 GLU U 131 " pdb="FE FE K 201 " model vdw 2.038 2.260 nonbonded pdb=" OE1 GLU R 131 " pdb="FE FE H 201 " model vdw 2.050 2.260 nonbonded pdb=" OE1 GLU Q 131 " pdb="FE FE J 201 " model vdw 2.066 2.260 ... (remaining 301939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 191) selection = (chain 'B' and resid 2 through 191) selection = (chain 'C' and resid 2 through 191) selection = (chain 'D' and resid 2 through 191) selection = chain 'E' selection = (chain 'F' and resid 2 through 191) selection = chain 'G' selection = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = (chain 'U' and resid 2 through 191) selection = chain 'V' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.610 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 83.900 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 34944 Z= 0.475 Angle : 0.727 10.232 46944 Z= 0.438 Chirality : 0.041 0.126 5040 Planarity : 0.003 0.024 6240 Dihedral : 18.436 84.084 13080 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 12.67 % Allowed : 16.08 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 4176 helix: -1.51 (0.07), residues: 3408 sheet: None (None), residues: 0 loop : -2.43 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2000 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 1544 time to evaluate : 4.181 Fit side-chains outliers start: 456 outliers final: 190 residues processed: 1756 average time/residue: 1.4630 time to fit residues: 3059.2541 Evaluate side-chains 1595 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1405 time to evaluate : 4.299 Switching outliers to nearest non-outliers outliers start: 190 outliers final: 80 residues processed: 115 average time/residue: 1.4508 time to fit residues: 205.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 83 GLN Z 182 HIS ** Z 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 4 GLN A 87 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 87 GLN E 182 HIS ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 83 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 87 GLN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 83 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN K 182 HIS ** K 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN M 182 HIS ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 83 GLN N 94 GLN N 147 ASN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 94 GLN O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN P 182 HIS ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN Q 83 GLN Q 87 GLN Q 108 ASN Q 182 HIS ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 GLN R 8 ASN R 83 GLN R 182 HIS S 8 ASN S 83 GLN S 94 GLN S 147 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 94 GLN T 147 ASN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 87 GLN ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN V 182 HIS ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 GLN W 83 GLN ** W 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 87 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 182 HIS ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34944 Z= 0.182 Angle : 0.537 5.802 46944 Z= 0.289 Chirality : 0.034 0.129 5040 Planarity : 0.003 0.023 6240 Dihedral : 4.151 13.986 4656 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 5.44 % Allowed : 28.39 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4176 helix: 0.97 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 744 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1800 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1604 time to evaluate : 3.935 Fit side-chains revert: symmetry clash outliers start: 196 outliers final: 113 residues processed: 1702 average time/residue: 1.5133 time to fit residues: 3049.7903 Evaluate side-chains 1554 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1441 time to evaluate : 4.224 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 77 residues processed: 38 average time/residue: 0.3360 time to fit residues: 28.7446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 182 HIS ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A 94 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 8 ASN C 182 HIS ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 182 HIS G 182 HIS H 4 GLN H 94 GLN H 108 ASN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 87 GLN I 94 GLN I 182 HIS J 4 GLN J 87 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN K 109 GLN K 182 HIS L 4 GLN L 182 HIS M 4 GLN M 109 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN Q 182 HIS R 4 GLN R 108 ASN R 182 HIS ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 147 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN U 108 ASN ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 182 HIS W 4 GLN W 94 GLN W 182 HIS ** W 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 80 GLN B 108 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 87 GLN D 94 GLN D 182 HIS ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 182 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34944 Z= 0.201 Angle : 0.530 5.851 46944 Z= 0.285 Chirality : 0.033 0.129 5040 Planarity : 0.003 0.026 6240 Dihedral : 3.943 14.533 4656 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.22 % Allowed : 32.11 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.13), residues: 4176 helix: 2.10 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.58 (0.21), residues: 744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1522 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 119 residues processed: 1600 average time/residue: 1.5266 time to fit residues: 2886.2136 Evaluate side-chains 1533 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1414 time to evaluate : 4.097 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 68 residues processed: 53 average time/residue: 0.5225 time to fit residues: 48.5533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 182 HIS ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 190 GLN G 94 GLN I 80 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN J 190 GLN K 4 GLN K 109 GLN K 182 HIS L 4 GLN L 94 GLN M 4 GLN M 87 GLN M 109 GLN N 8 ASN N 94 GLN N 147 ASN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 7 GLN P 87 GLN P 109 GLN ** P 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 GLN R 94 GLN S 8 ASN S 94 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 147 ASN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 8 ASN T 94 GLN T 147 ASN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN W 4 GLN B 4 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN F 80 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34944 Z= 0.351 Angle : 0.599 6.207 46944 Z= 0.318 Chirality : 0.037 0.126 5040 Planarity : 0.003 0.031 6240 Dihedral : 3.940 12.290 4656 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 6.14 % Allowed : 31.61 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.13), residues: 4176 helix: 2.36 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -1.10 (0.21), residues: 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1697 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1476 time to evaluate : 4.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 144 residues processed: 1559 average time/residue: 1.5845 time to fit residues: 2912.8169 Evaluate side-chains 1537 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1393 time to evaluate : 4.121 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 75 residues processed: 74 average time/residue: 0.5325 time to fit residues: 66.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A 94 GLN C 80 GLN C 83 GLN C 94 GLN E 80 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 94 GLN I 94 GLN J 94 GLN K 94 GLN K 109 GLN L 94 GLN M 109 GLN N 4 GLN N 94 GLN N 109 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN P 190 GLN Q 94 GLN Q 108 ASN R 8 ASN R 94 GLN S 4 GLN ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN T 94 GLN ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 94 GLN ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 GLN W 4 GLN W 80 GLN W 83 GLN W 94 GLN B 4 GLN B 80 GLN B 190 GLN D 109 GLN F 4 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34944 Z= 0.265 Angle : 0.583 6.606 46944 Z= 0.313 Chirality : 0.035 0.108 5040 Planarity : 0.003 0.038 6240 Dihedral : 3.870 12.010 4656 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.14 % Allowed : 31.86 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.13), residues: 4176 helix: 2.75 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1464 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 113 residues processed: 1553 average time/residue: 1.5824 time to fit residues: 2895.5402 Evaluate side-chains 1472 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1359 time to evaluate : 3.911 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 82 residues processed: 36 average time/residue: 0.6503 time to fit residues: 39.1515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 7.9990 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 4 GLN Z 94 GLN ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN C 83 GLN C 94 GLN E 4 GLN E 94 GLN G 94 GLN H 94 GLN H 108 ASN I 80 GLN I 94 GLN J 94 GLN K 8 ASN K 80 GLN K 94 GLN K 109 GLN L 4 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 94 GLN M 109 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN P 109 GLN ** Q 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Q 94 GLN R 94 GLN S 94 GLN S 109 GLN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 94 GLN ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN V 109 GLN W 4 GLN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN B 4 GLN B 94 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34944 Z= 0.209 Angle : 0.577 6.604 46944 Z= 0.312 Chirality : 0.034 0.103 5040 Planarity : 0.003 0.030 6240 Dihedral : 3.794 12.051 4656 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.86 % Allowed : 32.58 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.13), residues: 4176 helix: 3.12 (0.09), residues: 3384 sheet: None (None), residues: 0 loop : -0.64 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1643 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1468 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 103 residues processed: 1557 average time/residue: 1.6062 time to fit residues: 2952.0678 Evaluate side-chains 1479 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1376 time to evaluate : 4.133 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 81 residues processed: 27 average time/residue: 0.6197 time to fit residues: 30.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 GLN A 80 GLN A 94 GLN A 109 GLN A 147 ASN C 94 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 94 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 HIS K 94 GLN L 4 GLN L 94 GLN L 109 GLN L 147 ASN M 80 GLN M 94 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN Q 94 GLN ** R 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN R 94 GLN S 4 GLN S 80 GLN S 94 GLN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN T 109 GLN T 182 HIS ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN W 4 GLN W 83 GLN ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 80 GLN B 94 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 109 GLN D 147 ASN F 80 GLN F 94 GLN F 109 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34944 Z= 0.246 Angle : 0.608 5.822 46944 Z= 0.326 Chirality : 0.035 0.145 5040 Planarity : 0.003 0.047 6240 Dihedral : 3.773 11.644 4656 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.19 % Allowed : 33.92 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.13), residues: 4176 helix: 3.23 (0.09), residues: 3384 sheet: None (None), residues: 0 loop : -0.59 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1416 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 105 residues processed: 1498 average time/residue: 1.6278 time to fit residues: 2871.4388 Evaluate side-chains 1481 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1376 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 86 residues processed: 25 average time/residue: 0.6232 time to fit residues: 28.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 8 ASN Z 80 GLN ** Z 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN A 109 GLN C 80 GLN E 80 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 80 GLN H 94 GLN H 109 GLN I 80 GLN I 94 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN L 80 GLN L 147 ASN M 94 GLN M 109 GLN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 182 HIS ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN P 94 GLN P 109 GLN Q 80 GLN Q 94 GLN R 94 GLN R 148 HIS S 4 GLN S 94 GLN S 109 GLN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 GLN T 182 HIS ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 94 GLN ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 GLN V 94 GLN V 109 GLN W 4 GLN W 80 GLN W 83 GLN W 94 GLN W 148 HIS B 4 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 94 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34944 Z= 0.239 Angle : 0.628 6.648 46944 Z= 0.337 Chirality : 0.035 0.137 5040 Planarity : 0.003 0.053 6240 Dihedral : 3.766 12.049 4656 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.69 % Allowed : 35.03 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.13), residues: 4176 helix: 3.19 (0.09), residues: 3408 sheet: None (None), residues: 0 loop : -0.33 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1424 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 94 residues processed: 1501 average time/residue: 1.6310 time to fit residues: 2881.7915 Evaluate side-chains 1475 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1381 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 83 residues processed: 20 average time/residue: 1.1173 time to fit residues: 33.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 0.6980 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 94 GLN Z 147 ASN A 94 GLN A 109 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN I 4 GLN I 94 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN J 94 GLN J 147 ASN K 80 GLN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 HIS L 4 GLN L 109 GLN L 147 ASN M 80 GLN M 94 GLN M 109 GLN M 147 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 94 GLN N 109 GLN N 182 HIS ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN P 147 ASN P 148 HIS Q 94 GLN R 87 GLN R 94 GLN S 4 GLN S 80 GLN S 94 GLN S 182 HIS ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 HIS ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN V 147 ASN W 4 GLN W 94 GLN B 80 GLN B 94 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 109 GLN D 147 ASN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN F 94 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34944 Z= 0.235 Angle : 0.650 6.630 46944 Z= 0.348 Chirality : 0.035 0.141 5040 Planarity : 0.003 0.038 6240 Dihedral : 3.750 11.365 4656 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.78 % Allowed : 35.56 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.13), residues: 4176 helix: 3.13 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1375 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 95 residues processed: 1465 average time/residue: 1.6048 time to fit residues: 2774.9541 Evaluate side-chains 1470 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1375 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 83 residues processed: 20 average time/residue: 0.6860 time to fit residues: 25.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 1.9990 chunk 387 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 chunk 374 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 80 GLN Z 94 GLN A 80 GLN A 94 GLN A 109 GLN C 80 GLN E 80 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN H 94 GLN I 4 GLN I 80 GLN I 94 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 ASN L 80 GLN L 94 GLN L 147 ASN M 94 GLN M 109 GLN M 147 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN N 94 GLN N 109 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 80 GLN O 94 GLN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN P 94 GLN P 109 GLN Q 80 GLN Q 94 GLN Q 147 ASN R 80 GLN R 94 GLN S 4 GLN S 94 GLN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 80 GLN T 94 GLN T 182 HIS ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN U 148 HIS ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 GLN V 87 GLN V 94 GLN V 147 ASN ** W 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 GLN W 94 GLN W 147 ASN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 94 GLN D 147 ASN F 94 GLN F 109 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34944 Z= 0.244 Angle : 0.672 7.228 46944 Z= 0.360 Chirality : 0.035 0.137 5040 Planarity : 0.003 0.058 6240 Dihedral : 3.752 11.469 4656 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.36 % Allowed : 36.78 % Favored : 59.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.13), residues: 4176 helix: 3.14 (0.09), residues: 3432 sheet: None (None), residues: 0 loop : -1.00 (0.21), residues: 744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1378 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 89 residues processed: 1472 average time/residue: 1.6252 time to fit residues: 2811.4992 Evaluate side-chains 1430 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1341 time to evaluate : 3.947 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 85 residues processed: 12 average time/residue: 0.8683 time to fit residues: 18.9758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 94 GLN Z 109 GLN Z 147 ASN A 94 GLN E 94 GLN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN I 4 GLN I 94 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN K 80 GLN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 ASN L 94 GLN L 109 GLN L 147 ASN M 80 GLN M 94 GLN M 109 GLN M 147 ASN ** N 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 GLN ** N 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 GLN O 109 GLN ** O 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 GLN P 109 GLN Q 94 GLN Q 147 ASN R 94 GLN S 80 GLN S 94 GLN ** S 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 GLN U 94 GLN ** V 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN V 147 ASN W 4 GLN W 94 GLN B 94 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 109 GLN D 147 ASN F 80 GLN F 94 GLN F 109 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081015 restraints weight = 63276.110| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.14 r_work: 0.2879 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34944 Z= 0.283 Angle : 0.683 7.114 46944 Z= 0.364 Chirality : 0.036 0.133 5040 Planarity : 0.004 0.040 6240 Dihedral : 3.795 12.156 4656 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 37.44 % Favored : 59.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.13), residues: 4176 helix: 3.06 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -0.88 (0.21), residues: 720 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32165.64 seconds wall clock time: 560 minutes 41.08 seconds (33641.08 seconds total)